See your individual DM.
I always rule that melee weapons count as bodily contact. Most Devil/Demon/angels etc use weapon, so I see no point in the spell unless interpreted this way. ((although i can see other GM ruling differently)).
Now if the devil was to throw its sword at you, well range attack work just fine (although the +2 defection bonus to AC would still apply).
It's quite obvious that summoned devils are summoned. The ability is called summon after all. Plus, it works just like summon monster spells, which are summoning spells, so you made the right call there.
Protection from evil only mentions natural weapons in the "prevents bodily contact" part of its description, so if you stick to the rules as written, weapons will ignore that part of the spell. It helps against most critters, too, since most summoned critters, especially the lower-level ones, don't use weapons. And if the low-level spell doesn't work against high-level summoning magic, now that isn't such a horrible thing.
On the other hand, a ruling that includes all mêlée weapons, or even all physical attacks, in the protection isn't unreasonable, either.